BioC 3.4: CHECK report for OLIN on malbec1

Package: OLIN

Version: 1.52.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OLIN_1.52.0.tar.gz

StartedAt: 2017-04-15 00:13:05 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:14:04 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 59.6 seconds

RetCode: 0

Status:  OK

CheckDir: OLIN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OLIN_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/OLIN.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OLIN/DESCRIPTION’ ... OK
* this is package ‘OLIN’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OLIN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘convert’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ino: no visible global function definition for ‘locfit’
ino: no visible global function definition for ‘predict’
lin: no visible global function definition for ‘locfit’
lin: no visible global function definition for ‘predict’
oin: no visible global function definition for ‘gcvplot’
oin: no visible global function definition for ‘locfit’
oin: no visible global function definition for ‘predict’
olin: no visible global function definition for ‘gcv’
olin: no visible global function definition for ‘locfit’
olin: no visible global function definition for ‘predict’
Undefined global functions or variables:
  gcv gcvplot locfit predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
olin 16.968      0  16.985
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/OLIN.Rcheck/00check.log’
for details.

* installing *source* package ‘OLIN’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OLIN)

name	user	system	elapsed
anovaint	0.148	0.004	0.151
anovapin	0.084	0.000	0.084
anovaplate	0.116	0.000	0.116
anovaspatial	0.236	0.000	0.235
backgroundCorrect2	0.376	0.008	0.384
bas	0.116	0.000	0.117
colorbar.mxy	0.048	0.004	0.050
fdr.int	0.000	0.000	0.001
fdr.int2	0.000	0.000	0.001
fdr.spatial	0.000	0.000	0.001
fdr.spatial2	0	0	0
fgbg.visu	0.16	0.00	0.16
ino	0.180	0.020	0.199
lin	0.664	0.000	0.663
m2v	0.064	0.000	0.063
ma.matrix	0.232	0.004	0.235
ma.vector	0.428	0.008	0.437
mxy.abs.plot	0.172	0.000	0.175
mxy.plot	0.084	0.000	0.086
mxy2.plot	0.064	0.000	0.063
oin	0.94	0.00	0.94
olin	16.968	0.000	16.985
p.int	0.000	0.000	0.001
p.int2	0.000	0.000	0.001
p.spatial	0	0	0
p.spatial2	0.000	0.000	0.001
sig.mask	0.000	0.000	0.001
sigint.plot	0.000	0.000	0.001
sigint.plot2	0.000	0.000	0.001
sigxy.plot	0.000	0.000	0.001
sigxy.plot2	0.000	0.000	0.001
v2m	0.060	0.000	0.059